plotMeanSD: Plot Row Standard Deviations vs. Row Means

In roryk/bcbioRnaseq: RNA-Seq Utilities

Description

vsn::meanSdPlot() wrapper that plots log2(), rlog(), and varianceStabilizingTransformation() normalized counts.

Usage

plotMeanSD(object, ...)

## S4 method for signature 'bcbioRNASeq'
plotMeanSD(object, orientation = c("vertical",
  "horizontal"), legend = FALSE)

## S4 method for signature 'DESeqDataSet'
plotMeanSD(object, orientation = c("vertical",
  "horizontal"), legend = FALSE)

Arguments

object	Object.
...	Additional arguments.
orientation	Orientation to use for plot grid, either horizontal or vertical.
legend	Include the color bar legend. This is typically not that informative and is disabled by default, to improve the plot appearance.

Value

ggplot grid.

Author(s)

Michael Steinbaugh, Lorena Patano

See Also

Other Quality Control Functions: plot5Prime3PrimeBias, plotCorrelationHeatmap, plotCountDensity, plotCountsPerGene, plotDispEsts, plotExonicMappingRate, plotGenderMarkers, plotGeneSaturation, plotGenesDetected, plotIntronicMappingRate, plotMappedReads, plotMappingRate, plotPCACovariates, plotPCA, plotRRNAMappingRate, plotTotalReads

Examples

# bcbioRNASeq ====
plotMeanSD(bcb_small)

# DESeqDataSet ====
plotMeanSD(dds_small)

roryk/bcbioRnaseq documentation built on May 27, 2019, 10:44 p.m.